Omega Pirate in Metroid Prime, it's actually quite easy now thinking afterwards, you just have to avoid stuff, but back then it wasn't so easy with a small TV screen (14") and Metroid Prime's type of controls, which were quite clumsy at times (in my opinion).

Also more recently Deus Ex: Human Revolution and the first douchebag of a boss. I really want to play this game but the boss fights keep me off (if the following ones are as terrible). I've beaten him of course, but these boss fights just don't fit in the game (as everyone probably agrees).

Old King Allant from Demons' Souls and Dark Murai from Ninja Gaiden Sigma, took me a few years before I tried Dark Murai again 'cause I got so frustrated (I ran out of potions after the boss before, and there's no vendors to buy potions between the last two bosses).

Nemesis from Resident Evil. That scream, sudden appearances, Stars taunts. Keep in mind I was like 11 back then shit was the most scaring thing in existence. You didn't have the to kill him but doing so was pretty hard.

WHITNEYS MILTANK.
This thing was satans baby. Even with a traded Machop, a Geodude and a Onix, this thing would still flinch hax or crit.

FF13:
-The Eidolon battles. I mean really. In what universe is it considered good game design to have the difficulty spike THAT MUCH from normal gameplay.

- Proudclad V2. Never have i raged at a game so hard and sworn to never play it again for a good amount of time. I know i could definitely beat it, but doing so with a grouping that would require a 30 minute fight is not worth it.

Hardest boss with no restrictions doing everything I can to win, Theseus, God of War 2, Titan mode. Took me a couple hundred deaths to get past him.

Hardest boss with some restrictions is Vergil, DMC 3: Special Edition, Mission 20, Dante Must Die! mode. Basically, there's two easy ways to cheese him, (jump cancelling, quicksilver/item spam) and one really overpowered ability you can use to semi cheese him, (Royal Block) but if you don't use one of those, he's pretty much unbeatable. Vergil's patterns don't seem to change much from normal, but each difficulty after that knocks off a little bit of his hit stun timer. On DMD! mode if he blocks an attack, (which he will do randomly when you're trying to damage him) you no longer have enough time to jump or trickster away before he damages you. And considering he heals for a crap ton, and he can 3-5 shot you, trading hits with him is not a viable tactic without spamming healing items. The only way he could be beaten under these conditions is with insane luck. You can end combos early to avoid getting blocked, but this only works some of the time as he can block the first hit. The real problem though is that you need that dps time to out damage his healing or you get nowhere. Basically, you'd need to be able to see the future so you know when to stop attacking, when to do a full combo, and when to avoid hitting him entirely. It's possible I could beat him under those restrictions, but it would be due to very very good RNG, not me becoming a better player or learning something new about the fight. And even with incredible RNG, this is still a very difficult boss fight. Even if you try to cheese him with items he'll still kick your ass and serve it to you on a plate if you're not at least good enough to steamroll hard mode.

If Goku's power level increases at the same rate till the end of DBGT as it does till the end of the Frieza saga, as a SS4 Goku would have a PL of roughly 939 Quinoctogintillion. For reference that is a 260 digit number. A PL of 14,600 is required to destroy an earth sized planet. There are about 2 nonillion earths worth of mass in the universe. That means SS4 Goku can destroy the universe about 32 Octosexagintillion times over. There's a reason they made Goku a god at the end of GT.

Mass Effect 1: Tha Krogan boss very early on in the game.
At the start you get to chose which mission you want to do first, I chose this one and oh dear lord are you weak at the start of that game.
The game works weirdly anyway, early on it's stupidly difficult and then near the end it's facerollingly easy.
That Krogan guy would whoop my ass again and again and again and every time I had to go up the damned elevator and endure the terrible conversation.

Super Meat Boy: Brownie
You need to be super fast, make 0 mistakes and stay focused for a long level else redo the whole thing.
That said, that game was difficult as hell anyway.

Most older Final Fantasy bosses, they just took forever and ever to just die already.

Mass Effect 1: Tha Krogan boss very early on in the game.
At the start you get to chose which mission you want to do first, I chose this one and oh dear lord are you weak at the start of that game.
The game works weirdly anyway, early on it's stupidly difficult and then near the end it's facerollingly easy.
That Krogan guy would whoop my ass again and again and again and every time I had to go up the damned elevator and endure the terrible conversation..

Honestly, I just put that fight on Casual so I can faceroll past him and not have to deal with that goddamn elevator/conversation every single attempt.

But yeah, ME1 is funny like that, the first few missions are hard as shit but then it gets easy after about the mission you get Liara.

i was not crying in the shower
i just realized how i'll never get to meet darth vader and then soap got in my eye - Kylo Ren

Brock in Pokemon Yellow. I was a child (7 years old I believe) back then and well... tactics/strategy weren't my things. Let's say this fight changed me as a person a bit.

haha this brings back good memories. I remember having to lv my pikachu wayy past what you were supposed to in order to beat brock. I didn't know about catching other pokemon or any of that sort of thing.

To answer the question, any boss really in DMC 3 on Dante Must Die mode, some hard stuff. I couldn't do it but i was also younger when the game came out, so I may try it again soon.

Too many to list from Kingdom Hearts
Seymour Flux
Brock and Misty with Charmander as your starter in Gen1
Malygos.Particularly because he bugged out every time my guild took me.
Odin from FF13.Appropriately nicknamed "Odamn"Christopher Robin